The level of direct coordination between Al Qaeda's leadership in Pakistan and the group that originally was known as Al Qaeda in Iraq has always been limited - and has appeared pretty much dead since 2006. Though you can still find references to "AQI" in US government literature and press reports, the group has rebranded itself multiple times - first becoming the Mujahidin Shura Council, then charging its name to the Islamic State in Iraq in 2006. The group formally merged with jihadis in Syria last year and started calling itself the Islamic State in Iraq and the Levant (ISIS).

Zawahiri issued a letter last night on jihadi forums formally announcing the group he leads has no affiliation with the group (a translation is here). "(Al Qaeda) declares that it has no links to the ISIS group. We were not informed about its creation, nor counseled," the letter reads. "Nor were we satisfied with and we ordered it to stop. ISIS is not a branch of Al Qaeda and we have no organizational relationship with it."

The writing has been on the wall in this regard for some time. The forerunner of ISIS in Iraq resisted control by Al Qaeda as early as 2004, both in carrying out attacks on civilians that Zawahiri deemed counterproductive to his long term goals and in focusing on national and regional concerns, rather than the global ambition to confront the US and Israel.

It turns out that local armies, fighting local wars are more interested in their parochial concerns than Zawahiri's quixotic hope for a global jihad to remake the world order and that their commanders aren't particularly interested in taking their orders from a group based thousands of miles away.

Zawahiri has been trying to assert control over ISIS for over a year, with little success. Why he'd want to is obvious - they're currently a global magnate for Islamist fighters and they're fighting in the heart of the Middle East - rather than stuck on the distant margins of the Islamic world as Al Qaeda central is. But he's been mostly ignored. In 2013 the self-styled emir of ISIS Abu Bakar al-Baghdadi (a nom de guerre) claimed his group had merged with the Jabhat al-Nusra (JN), a Syria-based jihadi militia participating in the rebellion against President Bashar al-Assad.

Mr. Baghdadi's announcement contributed to rancor between ISIS and JN and other jihadis in Syria, a conflict within a conflict that rages to this day. Foreign fighters who were working with JN flocked to ISIS, while JN remained a more Syria-based organization. Competition for weapons and money led to outright conflict and assassinations between the groups.

This fitnah, or civil strife, was considered a great sin by Zawahiri and he feebly tried to end it. In June of last year he ordered the merger to be undone, rebuked Baghdadi, and told him his group should remain focused and based in Iraq. ISIS simply ignored Zawahiri, who was Al Qaeda's number two under Osama bin Laden and replaced him as boss after the US killed Bin Laden.

The Zawahiri letter that became public today focused on "fitnah" as the reason for his announcement. "We declare ourselves innocent of fitnah in (the Levant) between mujahideen and we declare our innocence of the blood that has been shed," the statement reads. "We call upon everyone to fear God... and to realize the catastrophe that happened to the Jihad in Syria and the future of this Muslim nation due to the fitnah that they are in."

ISIS has appeared more engaged in fighting fellow rebels of late than challenging Assad, and thousands have been killed in internecine rebel violence in the past month.

What does it mean? That depends on how much influence Zawahiri has on funders of the jihad, particularly in Gulf states like Saudi Arabia. His comments could see money redirected from ISIS to JN in Syria though ISIS controls many oil fields in Syria now, at least partially self-funding itself.

Charles Lister, a fellow at the Brookings Doha Center, thinks the announcement is important.

Asked if this meant that Al Qaeda no longer has an affiliate in Iraq, Lister wrote: "Essentially yes. Though that has (v) debatably been the case since the ISI’s formation."

This is of interest to me because of the way "Al Qaeda" is carelessly tossed around, in journalism and elsewhere (and, yes, I've been guilty). Just because a group is Sunni, carries out suicide bombings, and expresses an interest in creating an Islamic state they imagined would be governed by principles that prevailed 1,400 years ago, at the time of Islam's founding, doesn't make them "Al Qaeda" if that means "the group that organized the 9/11 attacks on the US."

Recent history has shown that most of the jihadis that emerged in the wake of the US invasion of Iraq had very little interest in pursuing the "far enemy." Kill American troops inside Iraq and advance their domestic agenda? Absolutely. Engage in a far-flung war, striking out at civilians indiscriminately far from home? That has not held much appeal for the Iraqi jihadis, at least on the evidence so far.

Zawahiri has never been able to bring the Iraqi fighters under his thumb. One of the earliest leaders of Al Qaeda in Iraq was the Jordanian Abu Musab al-Zarqawi (later killed in a US airstrike) and their tentative alliance came apart in 2005. In a letter to Zarqawi in 2005, Zawahiri's frustration was palpable.

"If we look at the two short-term goals, which are removing the Americans and establishing an Islamic emirate in Iraq, or a caliphate if possible, then we will see that the strongest weapon which the mujahedeen enjoy – after the help and granting of success by God – is popular support from the Muslim masses in Iraq, and the surrounding Muslim countries," he wrote then, warning of the "scenes of slaughter" of captives and civilians that the Iraqi group was daily carrying out. Zawahiri told Zarqawi that he was alienating the Iraqi people and undermining his cause.

Zarqawi and his followers ignored Zawahiri, increased the tempo of sectarian attacks targeting Shiite civilians, and created the conditions that saw many Sunni Iraqi tribes turn on them violently in 2007.

That history appears to be repeating itself in Syria - though with the added wrinkle of other jihadi groups like JN that may maintain longer term links with the Al Qaeda led by Zawahiri.